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EDIT: So I finally fixed the T flipflop, but now I've discovered that another major culprit is the 1 tick pulse generator, generator 2 tick pulses on occasion. That's what causes the red and orange faces to not function properly, if you attempt to turn them first. I have no idea how to fix this, other than tearing out the pulse generators and moving them to a new location, hoping that it'll work there. Redstone inconsistencies are location dependent.
MCforum thread: http://www.minecraftforum.net/topic/509338-working-rubiks-cube/
Save here: http://www.mediafire.com/?nto6l62n12dy7gr
Link to us http://360.mmgn.com/Videos/Minecraft-Working-Rubiks-Cube
Video by: Heller
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